LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
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### Pure diffusion with a reaction source term analog of a periodic  ###
### Poiseuille flow problem using transport DPD (tDPD) simulation    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### tDPD system setup follows Fig.1 in the publication:              ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis.          ###
### "Transport dissipative particle dynamics model for mesoscopic    ###
### advection-diffusion-reaction problems. J. Chem. Phys.,           ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254                        ###
########################################################################
units                   lj
dimension               3
boundary                p p p
neighbor                0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style              tdpd 2
comm_modify  vel yes

region     tdpd     block -10 10 -10 10 -5 5 units box
create_box          1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
  1 by 1 by 1 MPI processor grid
create_atoms        1 random 16000 276438 NULL
Created 16000 atoms
  using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
  create_atoms CPU = 0.002 seconds
mass                1 1.0
set                 atom * cc 1 1.0
Setting atom values ...
  16000 settings made for cc index 1
set                 atom * cc 2 1.0
Setting atom values ...
  16000 settings made for cc index 2

pair_style          tdpd 1.0 1.58 9872598
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0

compute             mythermo all temp
thermo              50
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

fix         mvv     all mvv/tdpd 0.5
fix         upper1  all tdpd/source 1 cuboid 0.0  5.0 0.0 20.0 10.0 10.0  0.01
fix         lower1  all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix         upper2  all tdpd/source 2 cuboid 0.0  5.0 0.0 20.0 10.0 10.0 -0.01
fix         lower2  all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0  0.01

timestep            0.01
run                 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair tdpd command: doi:10.1063/1.4923254

@Article{ZLi2015_JCP,
 author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
 title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
 journal = {The Journal of Chemical Physics},
 year = {2015},
 volume = {143},
 number = {1},
 pages = {014101}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.78
  ghost atom cutoff = 1.78
  binsize = 0.89, bins = 23 23 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair tdpd, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.51 | 12.51 | 12.51 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1              48.942039      0              50.441946      201.70031    
        50   1.011026       43.947278      0              45.463722      194.91628    
       100   1.0038328      43.75705       0              45.262706      197.34972    
       150   1.0024595      43.731513      0              45.235109      196.71302    
       200   0.99175816     43.70274       0              45.190285      194.60811    
       250   0.99533515     43.714618      0              45.207528      197.48663    
       300   0.99335422     43.711138      0              45.201076      196.84197    
       350   1.0012089      43.71311       0              45.214829      193.04504    
       400   1.0085738      43.717565      0              45.230331      197.2073     
       450   0.99147043     43.722807      0              45.209919      200.14351    
       500   1.0005014      43.717024      0              45.217682      197.81942    
Loop time of 59.9704 on 1 procs for 500 steps with 16000 atoms

Performance: 7203.552 tau/day, 8.337 timesteps/s, 133.399 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 53.892     | 53.892     | 53.892     |   0.0 | 89.86
Neigh   | 5.3558     | 5.3558     | 5.3558     |   0.0 |  8.93
Comm    | 0.34774    | 0.34774    | 0.34774    |   0.0 |  0.58
Output  | 0.00089543 | 0.00089543 | 0.00089543 |   0.0 |  0.00
Modify  | 0.30481    | 0.30481    | 0.30481    |   0.0 |  0.51
Other   |            | 0.06955    |            |       |  0.12

Nlocal:          16000 ave       16000 max       16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          14049 ave       14049 max       14049 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         749053 ave      749053 max      749053 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749053
Ave neighs/atom = 46.815812
Neighbor list builds = 184
Dangerous builds = 0
reset_timestep      0

compute     cc1     all tdpd/cc/atom 1
compute     cc2     all tdpd/cc/atom 2
compute     bin     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile

run                 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 13.01 | 13.01 | 13.01 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.0005014      43.717024      0              45.217682      199.49297    
        50   0.99569204     43.716832      0              45.210276      197.52311    
       100   0.99430734     43.714806      0              45.206174      197.74323    
Loop time of 12.1636 on 1 procs for 100 steps with 16000 atoms

Performance: 7103.169 tau/day, 8.221 timesteps/s, 131.540 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 10.931     | 10.931     | 10.931     |   0.0 | 89.87
Neigh   | 1.0581     | 1.0581     | 1.0581     |   0.0 |  8.70
Comm    | 0.071199   | 0.071199   | 0.071199   |   0.0 |  0.59
Output  | 0.00016157 | 0.00016157 | 0.00016157 |   0.0 |  0.00
Modify  | 0.088319   | 0.088319   | 0.088319   |   0.0 |  0.73
Other   |            | 0.01448    |            |       |  0.12

Nlocal:          16000 ave       16000 max       16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          14065 ave       14065 max       14065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         749621 ave      749621 max      749621 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749621
Ave neighs/atom = 46.851312
Neighbor list builds = 36
Dangerous builds = 0
Total wall time: 0:01:12
